Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397918.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1223.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14297
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.22
Warning! 6121 characters in sequence are not A, C, G, or T
Found at i:728 original size:171 final size:171
Alignment explanation
Indices: 464--860 Score: 451
Period size: 171 Copynumber: 2.3 Consensus size: 171
454 TTTTAGAGCA
* * *
464 AGTAATAAGGCTTTTGAAGGAATGAGTTACTATAAA-AGGACTATTCTTGTCAATGAATGCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATA-GACTTTTCTTGCCAATGAATGCTTTT
* * * * *
528 TTTCTCACATTTTCCCAAGCAGGCATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAATATT
65 TCTCTCACATTTTCCCAAGCAGACATTCAATTACAATCTGTTTTAACCAAAAATGTAAAAAAATT
* ** * *
593 GAACTTAAAATCAACTATGAGATTATAAAATCATTTAACGTG
130 CAACTTAAAATCAACTATGAGATTATAAAATCAAGTAAAGCG
* * * *
635 AGTAGTAAGGCTTTTGAAGGAATGGGTGATTATAAATAGACTTTTCTTGCCAATGAGTGGCTTTT
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAAT-GCTTTT
* ** * * *
700 TCTC-CAC-GTTTCTTGAAGTAGACATTCAATTACAATTTGTTTTAACCAAAAGTGTAAAAAAAT
65 TCTCTCACATTTTC-CCAAGCAGACATTCAATTACAATCTGTTTTAACCAAAAATGTAAAAAAAT
** *
763 TCAACTTAAAATTTATTATGAGATTATAAAATCAAGTAAAGCG
129 TCAACTTAAAATCAACTATGAGATTATAAAATCAAGTAAAGCG
* * * * * *
806 AGTAATTAGGCTTTCGAAGGCATGAGTGACTACAAATGGAC-TTTCTTACCAATGA
1 AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGA
861 TTACCTTTCT
Statistics
Matches: 188, Mismatches: 35, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
170 17 0.09
171 161 0.86
172 10 0.05
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATAGACTTTTCTTGCCAATGAATGCTTTTT
CTCTCACATTTTCCCAAGCAGACATTCAATTACAATCTGTTTTAACCAAAAATGTAAAAAAATTC
AACTTAAAATCAACTATGAGATTATAAAATCAAGTAAAGCG
Found at i:6792 original size:171 final size:172
Alignment explanation
Indices: 6484--6800 Score: 399
Period size: 171 Copynumber: 1.8 Consensus size: 172
6474 ACCCATACCT
* ** * *
6484 TCGAAAGCCTCATTACTCATTTTAAATGATTTTATAATCTCATAATTGATTTTATGTTGAATTAT
1 TCGAAAGCCTCATTACTCACTTTAAAAAATTTTATAATCTCAAAATTGATTTTAAGTTGAATTAT
* * * * * *
6549 TTTTACATTTTTTGTTAAAACAATCTATAATTCAGCGTCTACCCTGAAAAATATGAAGAAAATGG
66 TTTTACATTTTTGGTTAAAACAATCTATAATTCAACGTCTACCCTCAAAAACATGAAGAAAAAGC
6614 AATTCATTCGG-AAGAAAAGTTCAGTTATCATCACTCGTGCCC
131 AATTCATT-GGTAAGAAAAGTTCAGTTATCATCACTCGTGCCC
* * * *
6656 TCGAAAGCCTTATTACTCCCTTTAAAAAATTTTATGATCTCAAAATTGATTTTAAGTTGTATT-T
1 TCGAAAGCCTCATTACTCACTTTAAAAAATTTTATAATCTCAAAATTGATTTTAAGTTGAATTAT
* * * *
6720 TTTTACATTTTTGGTTAAAACAAAT-TGTAATTGAATGTCTA-CCTCAAGAAACGTGAAGAAAAA
66 TTTTACATTTTTGGTTAAAAC-AATCTATAATTCAACGTCTACCCTCAA-AAACATGAAGAAAAA
*
6783 GCCATTCATTGGTAAGAA
129 GCAATTCATTGGTAAGAA
6801 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
170 7 0.06
171 58 0.48
172 57 0.47
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (172 bp):
TCGAAAGCCTCATTACTCACTTTAAAAAATTTTATAATCTCAAAATTGATTTTAAGTTGAATTAT
TTTTACATTTTTGGTTAAAACAATCTATAATTCAACGTCTACCCTCAAAAACATGAAGAAAAAGC
AATTCATTGGTAAGAAAAGTTCAGTTATCATCACTCGTGCCC
Found at i:8229 original size:171 final size:170
Alignment explanation
Indices: 7740--8977 Score: 1178
Period size: 171 Copynumber: 7.2 Consensus size: 170
7730 NNNNNNNNNN
* * **
7740 TTATAATCTCATAATTGATTTTATGTTGAATTGTTTTTACATTTTTGATTAAAATACCTTATAAT
1 TTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTTACATTTTTGATTAAAACAAATTATAAT
* * ** * ** * *
7805 TAAATGTCTGGCTTGGGAAATGTGAAGAAAAAGGGATTCATTG-GCAAGAACAGTCCATTTATCG
65 TGAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGAG-AA-AAAAGTCCATTTATAG
* * *
7869 TCACCCATTCCTTCGAAAGCCTTACTATTCACTTTAAATGGTT
128 TCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
* * * *
7912 TTATAATCTCAAAATTGATTTTAAGTTGCATTTTTTTTTACATTTTTGGTTAAAATAAATTATAA
1 TTATAATCTCATAATTGATTTTAAGTTG-A-ATTTTTTTACATTTTTGATTAAAACAAATTATAA
* * * * *
7977 TTCAATGTCTACCTCAAGAAACATGAAGAAAAAGCCATTCACTG-GCAAGAAAAGTCCATTTATA
64 TTGAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGAG-AA-AAAAGTCCATTTATA
* * *
8041 GTCACTCATTTCTTCAAAAGCCTTATTACTCGCTTTAAATGGTT
127 GTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
* * * *
8085 TTATATTCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAATAGATTACAATT
1 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAAATTATAATT
* * * * * * *
8150 AAATGTGTACCTTGAGAAACGTGAAGAAAAAGACATTCATTGAGAAACAAAATTCATTTATAGTC
66 GAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGAGAAA-AAAGTCCATTTATAGTC
*
8215 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAACT-ATT
130 ACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA-TGGTT
* * * * * *
8256 GTATAATCACATAATTTATTTTAAGTCGAATATTTTTACATTTTT-AGTTAAAACAACTTATAAT
1 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGA-TTAAAACAAATTATAAT
* * * * * ***
8320 TGAATGTATGTCTTAAGAAACGTAAAGAAAAAGGCTTTCATTGACTTGAAAAGTCCATTTATAGT
65 TGAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGA-GAAAAAAGTCCATTTATAGT
* ** * * * * *
8385 CATCTGTTCTTTCAAAATCTTTATTACTTATTTTAAATGGTT
129 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
** * * * *
8427 TTATAATCTCATAATAAATTTTAAGTTGCATTTTTTTTACATTTTAG-TTAAAAGAGATTATAAT
1 TTATAATCTCATAATTGATTTTAAGTTG-AATTTTTTTACATTTTTGATTAAAACAAATTATAAT
* * * * ** * * * *
8491 TGAATGGCTACCTTTACATGCATTAAGAAAAAGCCATTCATTGACTAAAAAGGTCCATTTATAGT
65 TGAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGA-GAAAAAAGTCCATTTATAGT
* * * ** *
8556 TACCTATGCCTTTGAAAGCCTTGTTACTCACTTTAAATGGTT
129 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
* * * *
8598 TTAT-ATCCACATAATTAATTTTAAGTTTAATTTTTTTATATTTTTGATTAAAACAAATTATAAT
1 TTATAAT-CTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAAATTATAAT
* * ** * * * *
8662 TGAATGTTTGTCTTGGGAAAGGTGAAGAAAAAGTCATTCATT-AGCAAAAAAGTCCTTTTATGGT
65 TGAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGAG-AAAAAAGTCCATTTATAGT
* * * *
8726 CACGCATTCCTTCAAAAGCTTTATTACTCGCTTTAAATAGTT
129 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
* ** *
8768 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTCACATTTTTGGCTAAAACAAACTATAATT
1 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAAATTATAATT
* * * * * * *
8833 GAATGTTTGCCTCAACAAATGTGAAGAAAAAGCAATTCATTTGTA-ATAAAAGCCCATTTATAGT
66 GAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCA-TTG-AGAAAAAAGTCCATTTATAGT
** * * * * *
8897 CGTCCATACTTTCAAAAGCCTCATTAATCACTTTAAATGATT
129 CACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
* * *
8939 TTATAATCTCATAACTGATTTTGAGTTGAATTTCTTTAC
1 TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAC
8978 NNNNNNNNNN
Statistics
Matches: 865, Mismatches: 184, Indels: 35
0.80 0.17 0.03
Matches are distributed among these distances:
170 154 0.18
171 520 0.60
172 44 0.05
173 145 0.17
174 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (170 bp):
TTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAAATTATAATT
GAATGTCTGCCTTAAGAAACGTGAAGAAAAAGCCATTCATTGAGAAAAAAGTCCATTTATAGTCA
CCCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTT
Found at i:13946 original size:21 final size:21
Alignment explanation
Indices: 13922--13962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13912 TCAAAAATGT
13922 GAAGCAAAAG-CCATTCATAGG
1 GAAG-AAAAGTCCATTCATAGG
*
13943 GAAGAAAAGTCCATTTATAG
1 GAAGAAAAGTCCATTCATAG
13963 TCTCCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (21 bp):
GAAGAAAAGTCCATTCATAGG
Done.